Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 8 | 16.88 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HLINHCAJ_3 | 139919 | 140512 | tmrB | ARO:3003059 | tmrB | 96.95 | 100.00 | AL009126.3 |
| HLINHCAJ_9 | 94333 | 94650 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| HLINHCAJ_9 | 93995 | 94333 | ykkC | ARO:3003063 | ykkC | 99.11 | 100.00 | AL009126.1 |
| HLINHCAJ_3 | 92047 | 93486 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| HLINHCAJ_47 | 11950 | 13152 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| HLINHCAJ_67 | 9386 | 11956 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| HLINHCAJ_36 | 9052 | 10221 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| HLINHCAJ_59 | 2713 | 3567 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| HLINHCAJ_59 | 2713 | 3565 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| HLINHCAJ_3 | 79236 | 80155 | mph(K) | Spiramycin, Telithromycin | 97.61 | 99.89 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HLINHCAJ_59 | 2713 | 3564 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| HLINHCAJ_16 | 28941 | 30581 | vmlR | ABC-F type ribosomal protection protein VmlR | INTERNAL_STOP | 97.62 | 100.00 | WP_003234144.1 |
| HLINHCAJ_17 | 25401 | 25919 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| HLINHCAJ_58 | 60931 | 62073 | capA | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | NP_391469 |
| HLINHCAJ_58 | 59267 | 60448 | capB | 0.0 | Capsule | Immune modulation | 99.58 | 100.00 | NP_391471 |
| HLINHCAJ_68 | 73242 | 74180 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391077 |
| HLINHCAJ_68 | 69570 | 70355 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| HLINHCAJ_45 | 21412 | 23175 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| HLINHCAJ_58 | 60463 | 60912 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| HLINHCAJ_68 | 74200 | 81336 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.03 | 100.00 | NP_391076 |
| HLINHCAJ_68 | 70381 | 71577 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.58 | 100.00 | NP_391079 |
| HLINHCAJ_31 | 97594 | 98235 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 97.82 | 100.00 | NP_390062 |
| HLINHCAJ_68 | 71595 | 73214 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.78 | 100.00 | NP_391078 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| HLINHCAJ_28 | 31704 | 32840 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| HLINHCAJ_21 | 11185 | 10316 | pdxS | 1.94e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| HLINHCAJ_32 | 195955 | 196731 | CodY | 2.84e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HLINHCAJ_40 | 185862 | 186431 | ClpP | 1.50e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HLINHCAJ_30 | 9666 | 10058 | spxA1 | 3.54e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HLINHCAJ_30 | 9666 | 10058 | spx | 2.11e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HLINHCAJ_43 | 20535 | 20777 | SpoVG | 4.75e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HLINHCAJ_16 | 75760 | 75563 | CspA | 1.37e-31 | cold shock protein | 89.39 | 100.00 | CAA62903 |
| HLINHCAJ_31 | 85742 | 85548 | CspD | 3.36e-28 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| HLINHCAJ_31 | 85742 | 85545 | CspB | 6.96e-28 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| HLINHCAJ_16 | 75760 | 75566 | CspR | 4.30e-27 | cold shock protein | 80.00 | 98.48 | AAO82613 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| HLINHCAJ_4 | 5460 | 5653 | Col(SD853) | 194 / 194 | 97.94 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HLINHCAJ_1 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_2 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_3 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_4 | 1.0 | 0.0 | 1.0 |
| HLINHCAJ_5 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_8 | 1.0 | 0.0 | 1.0 |
| HLINHCAJ_9 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_10 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_12 | 1.0 | 0.0 | 1.0 |
| HLINHCAJ_13 | 1.0 | 0.0 | 1.0 |
| HLINHCAJ_14 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_15 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_16 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_17 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_18 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_19 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_21 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_22 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_23 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_24 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_25 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_26 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_27 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_28 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_29 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_30 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_31 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_32 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_33 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_34 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_35 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_36 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_37 | 1.0 | 0.0 | 1.0 |
| HLINHCAJ_38 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_39 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_40 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_41 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_42 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_43 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_44 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_45 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_46 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_47 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_48 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_50 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_51 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_53 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_54 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_55 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_56 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_57 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_58 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_59 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_61 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_62 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_63 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_64 | 1.0 | 0.0 | 1.0 |
| HLINHCAJ_66 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_67 | 0.0 | 1.0 | 0.0 |
| HLINHCAJ_68 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HLINHCAJ_9 | 38093 | 64509 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| HLINHCAJ_24 | 133325 | 142460 | False | Siphoviridae | VOG0221, VOG4602, VOG8483, VOG9667, VOG9667, VOG0806, VOG4322, VOG4552, VOG1878, VOG4600 |
| HLINHCAJ_24 | 150389 | 174726 | False | Myoviridae | VOG4681, VOG0796, VOG10227, VOG0720, VOG4555, VOG4572, VOG1643, VOG4564, VOG4623, VOG1353, VOG1881, VOG1883, VOG1352, VOG4699, VOG1350, VOG6163, VOG1956, VOG1433, VOG1348, VOG0573, VOG4550, VOG4691, VOG4845, VOG7718, VOG3390, VOG4705, VOG0753 |
| HLINHCAJ_32 | 320166 | 343243 | False | Myoviridae / Siphoviridae | VOG5070, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG3129, VOG0275, VOG7930, VOG8610, VOG7895, VOG3390, VOG7718, VOG5534, VOG6940, VOG9713 |
| HLINHCAJ_66 | 49436 | 53601 | False | Unknown | VOG4551, VOG0025, VOG7476 |
Phigaro v2.4.0 (Database: Jan. 2024 release)